deseq dataset from star
Hi,
I have multiple count tables generated by star (using --quantMode). Is it possible to import these tables into deseq2 using DESeqDataSetFromHTSeqCount function or I need to create a matrix table and import using DESeqDataSetFromMatrix function? the tables look like this:
N_unmapped 2399497 2399497 2399497
N_multimapping 5671935 5671935 5671935
N_noFeature 18272205 33941344 34175527
N_ambiguous 786927 66964 66285
ENSOARG00000017577 296 141 155
ENSOARG00000020430 7 5 2
ENSOARG00000017587 8 4 4
ENSOARG00000025485 3 1 2
Thanks, Kisun
1 answer
I usually use:
dds<-DESeqDataSetFromMatrix(counts,colData=conditions,design =~ treatment + tissue)
on a matrix I have made in featureCounts. 'conditions' is a matrix where each row is a sample ID and corresponds to a column in 'counts' (I think these have to be ordered the same), and contains multiple variables that can be used in the design, e.g. here there are two columns in the 'conditions' matrix, 'treatment' and 'tissue'. After this I just run
ddseq<-DESeq(dds)
Any questions feel free to ask.
• 0 views
•
link
written
by
bruce.moran
Log in to answer this question.
You probably have to remove 2 columns and those upper
N_lines to use DESeqDataSetFromHTSeqCount